User:Wayne Decatur/Chem791A Work Session

Introduction

 * Lac Repressor at Wikipedia
 * Jmol
 * 1rpu at PDB
 * FirstGlance in Jmol
 * Lac repressor at Proteopedia
 * Proteopedia - a scientific 'wiki' bridging the rift between 3D structure and function of biomacromolecules, Eran Hodis, Jaime Prilusky, Eric Martz, Israel Silman, John Moult and Joel L Sussman. Genome Biology 9:R121, August 2008 or doi:10.1186/gb-2008-9-8-r121

Types of pages

 * Proteopedia:Topic Pages
 * Lac repressor at Proteopedia is an example of a topic page.
 * |Video on seeded vs. topic pages at Proteopedia
 * 1rpu is a seeded page.
 * 1eve is a seeded page that had been expanded.
 * Help:Searching
 * User:Eric Martz is a user page at only he can edit.
 * Special:RequestAccount
 * User:Eric Martz/Nucleosomes is a protected page that is a subpage of a user. It is authored by that user and only editable by that user.
 * User:Wayne Decatur
 * User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing is another example of a protected user subpage.
 * Help:Protected Pages tells how to create protected subpages of your user page.
 * Teaching Strategies Using Proteopedia describes using temporary sandbox pages for practice or experimenting or colloboration.

Authoring pages

 * Movies Showing How to Author Proteopedia Pages
 * Help:Editing
 * Special:Upload List of allowed file types: png, jpg, jpeg, tiff, tif, gif, mgif, pdb, cif, mmcif, cml, mol, xyz, kin, mmol

Authoring scenes within pages

 * Molecular Scene Authoring Tools
 * Example of scenes without and with transitions
 * User:Tom Gluick/glutamine synthetase (University of Maryland, Baltimore County). Includes instructions for using Jmol commands in the Jmol console for advanced scene authoring.

Advanced Scene Authoring
Be prepared to do some troubleshooting to get the exact scene you need. Keep in mind this an evolving and improving system and that some means of generating aspects of scenes outside of Proteopedia's Scene authoring tools might not be saved in the scene information properly by Proteopedia's Scene Authoring Tools. I have found this to be the case with instances involving representations that use 'isosurface', 'dots', and 'configuration' settings. For the problematic instances I mention, I found that troubleshooting simply involved either using a state script or Proteopedia's own Scene Authoring Tools to get close to the scene I want and then using the Jmol console to execute the problematic commands bypasses the errors I was encountering. SAVE OFTEN!
 * Scripting molecular views directions as found a Jmol Tutorial Authoring Tools talks about the variations you can use to get your desired scene; see the next entry as well.
 * Scripting in FirstGlance in Jmol directions as found a Jmol Tutorial Authoring Tools (JTAT) also has more information on going from scenes generated in FirstGlance in Jmol to a state script and this approach can be adapted to going from FirstGlance in Jmol scenes to Proteopedia scenes, the important point being to be use consistent version of Jmol.
 * Jmol Protein Explorer's powerful Quickviews approach really helps quickly generate particular scenes or ideas for scenes to generate elsewhere. Using the information detailed at the JTAT site on extracting state scripts, it is possible to go from these views to Proteopedia scenes; however, as the version of Jmol differs there may be slight discrepancies.

Advanced Jmol Scripting

 * Jmol interactive scripting documentation
 * Jmol documentation, features illustrated and detailed surface options

Other student projects and teaching resources in Proteopedia

 * Student Projects
 * Teaching Scenes, Tutorials, and Educators%27 Pages